LB 20-212 - Estimation of eDNA shedding and decay rates for muskellunge (Esox masquinongy) in early developmental stages and preliminary field assessment of eDNA methods

Background/Question/Methods:

Reliable detection and enumeration of imperiled species is critical to the development and implementation of restorative management strategies. For muskellunge (Esox masquinongy), an apex predator of ecological and recreational importance whose populations in the Upper St. Lawrence River are threatened by a variety of factors including disease and habitat loss, traditional approaches to population and distribution estimations are complicated by the species’ low density and elusive behavior. To improve the management of this species, we seek to determine the extent to which environmental DNA (eDNA) methodologies can complement traditional monitoring approaches. Because the identification and preservation of pristine spawning and nursery habitat being utilized by young muskellunge is essential to existing management initiatives, we investigated rates of eDNA release (shedding) and degradation (decay) originating from early developmental stages of the species in a controlled setting, with the intent that these rates be used to inform future quantitative abundance estimates from environmental samples. We also paired eDNA sampling in the river with traditional monitoring approaches (i.e., live capture) to determine the practicality of eDNA monitoring for muskellunge in a field setting and assess which types of surveys may benefit from complementary eDNA data collection.

Results/Conclusions:

We developed a specific qPCR assay targeting the muskellunge cytochrome oxidase I (COI) gene which can be multiplexed with an internal control to assess DNA recovery in the extraction process and identify inhibition. We estimated eDNA shedding rates for larval and juvenile muskellunge ranging from 5.10 × 10⁴ to 3.86 × 10⁵ copies/hour/gram fish and found no statistically significant difference in the shedding rates between the two life stages. Per-hour decay rate constants differed significantly between the two life stages, ranging from 0.064 to 0.131 for juveniles and 0.184 to 0.259 for larvae. Fertilized embryo did not release quantifiable amounts of DNA, and thus shedding and decay rates were not estimated. Water samples collected from five suspected spawning bays yielded eDNA detection rates between 80% and 100% and quantification rates of between 13% and 53%. Trap netting capture rates (muskellunge captures per trap night) for the same period of the spring spawning season ranged from 0% to 4.3%. The enumeration of shedding and decay rates for young muskellunge provides fundamental information for the interpretation of future data from a quantitative perspective and the successful detection and quantification of muskellunge DNA from environmental samples encourages continued investigation.